NGS tumor profiling for oncology from MedGenome
Dr. Chaitanya Ekkirala, Lab Director, NGS Operations, MedGenome Inc
The discovery of the genetic and epigenetic mechanisms underlying the development and progression of many diseases, including cancer, has helped redefine the paradigms of clinical research, diagnosis and treatment. Oncology research and diagnostics next generation sequencing (NGS). NGS improves rationally designed, personalized cancer treatments by identifying novel cancer mutations, detecting circulating tumor DNA (ctDNA), and discovering mutations responsible for hereditary cancer syndromes Did. With NGS, it is now possible to sequence whole genomes, whole exomes, whole transcriptomes, or just targeted genes to provide a detailed genomic landscape of many cancers.
med genome is committed to providing the highest quality NGS services for research and clinical development. Equipped with state-of-the-art sequencing platforms such as NovaSeq, MiSeq, and 10X Chromium Controller, our expert scientific team and lab facilities guarantee highly optimized protocols, customized solutions, and rapid turnaround times. increase.
Targeted panels for oncology mutational profiling using TSO-500
MedGenome is TruSight Oncology 500 from (TSO-500) IlluminaTSO-500 is a pan-cancer NGS assay with wide availability, rapid turnaround times, and a standardized bioinformatics pipeline to identify key genomic signatures for clinical research and immuno-oncology. This panel includes 523 cancer-associated gene variants and 55 RNA variants, providing comprehensive coverage of frequently mutated biomarkers (Figure 1) across multiple cancer types.
Assays are designed to detect
- • Single Nucleotide Variant (SNV)
- • Insert/Delete (InDels)
- • Copy number variation (CNV)
- • Novel transcriptional fusion
- • Splice variants
In addition, the TSO-500 panel has also reported key immunotherapeutic biomarkers. Tumor mutational burden (TMB) and the Microsatellite Instability (MSI) A condition that correlates with response to immune checkpoint inhibition.
The TSO-500 employs a single, highly standardized integrated workflow for both DNA and RNA input materials. Library preparation involves a hybridization capture-based target enrichment strategy. High analytical specificity is achieved by adding a unique molecular identifier (UMI) during library preparation. Low variant allele frequency (VAF) and suppress errors at the same time. Sequencing reactions are performed using fluorescently labeled oligonucleotides and off-the-shelf bioinformatics pipelines yield robust and reliable results.
- • Variety of sample types and throughput
MedGenome offers flexible and scalable genomic profiling from tumor biopsies, FFPE tissues, and liquid biopsies (to detect ctDNA) using the Illumina TruSight Oncology 500 portfolio (Figure 2). The platform also enables the analysis of sample sizes ranging from 8 to 192 samples and also enables accurate detection of low-volume input samples (from 30 ng of DNA and 40 ng of RNA input material).
- • Easy ctDNA detection from liquid biopsies
Noninvasive plasma-based assays have emerged as an important complementary diagnostic approach to tissue-based assays and are not suitable for repeated sampling or inaccessible tissues. Moreover, a single biopsy lacks information on tumor heterogeneity. Plasma contains tumor cell fragments and DNA from apoptotic or necrotic cancer cells that provide information about cancer aggressiveness, progression, and treatment outcome.of TSO-500 ctDNA This assay enables non-invasive, comprehensive genomic profiling of ctDNA from a simple blood draw, assessing over 500 gene variant classes in a single assay.
- • Optimized data analysis
The variant calling algorithm is optimized to eliminate errors, artifacts, and germline variants, resulting in high accuracy and analytical specificity (99.9998%). Data interpretation and reporting are powered by the PierianDx Clinical Genomics Workspace (CGW). CGW filters and prioritizes biologically relevant variants and provides automated and customizable genomic reports.
- • Accurate TMB and MSI analysis
The TSO-500 assay was error corrected Sequence and information pipeline It provides an accurate quantitative score of MSI status and an accurate and reproducible TMB value. The TMB calculation includes measurements of non-synonymous and synonymous SNVs and InDels based on specific criteria. This result was shown to be highly consistent with whole-exome studies.
- • High sensitivity
We used the TSO-500 platform to provide sensitive variant detection of CNV, with a detection limit of 2.2-fold fold change. Additionally, the TSO-500 library preparation protocol implements high binding specificity to hybridize to targets containing small mutations and SNVs, even from low-quality DNA samples and FFPE tissues. Assay reproducibility has been validated with FFPE samples as low as 5% VAF. Furthermore, in terms of RNA fusion detection, the hybrid capture method accurately captures gene fusions from both known and novel fusion gene partners, even from FFPE samples with RNA yields >= 40ng.
Advantages of MedGenome
MedGenome provides end-to-end customized solutions for comprehensive genomic profiling of small and large tumor samples to accelerate clinical and diagnostic research and development. We have the expertise to process and DNA sequence different types of samples including biopsies, FFPE tissues (DNA and RNA) and plasma (ctDNA). Our scientific team can also provide solutions for challenging sample processing and high-throughput his samples.
Utilize TruSight Target Panels to offer unique services and benefits.
- • Multiplexing Solution – Save time and samples by analyzing multiple tumor variant types for 523 genes in a single assay
- • speed – Streamlined and validated workflow with fast turnaround time for TSO-500 assays
- • A powerful bioinformatics pipeline – Additional insight into drug-gene interactions, actionable mutation identification, and comprehensive reporting
- • High Throughput Processing – Scientific expertise and state-of-the-art lab facilities for large sample sizes suitable for clinical research
- • TST170 panel for ctDNA – We validated the TruSight Tumor 170 panel with ctDNA samples for SNVs and indels in 151 genes, amplification in 59 genes, and fusion and splice variants in 55 genes.
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- 1. Zhao, Chen & Jiang, Tingting & Ju, Jin & Zhang, Shile & Tao, Jenhan & Fu, Yao & Lococo, Jenn & Dockter, Janel & Pawlowski, Traci & Bilke, Sven. (2020). TruSight Oncology 500: Enables comprehensive genomic profiling and biomarker reporting with targeted sequencing. 10.1101/2020.10.21.349100.
- 2. https://sapac.illumina.com/content/dam/illumina-marketing/documents/products/technotes/trusight-umi-rare-variant-technote-1000000050426.pdf
- 3. https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/trusight-oncology-500-data-sheet-m-gl-00173/trusight-oncology-500-and- ht-data-sheet-m-gl-00173.pdf
- 4. Wei, B., Kang, J., Kibukawa, M., Arreaza, G., Maguire, M., Chen, L., Qiu, P., Lang, L., Aurora-Garg, D., Cristescu , R., and Levitan, D. (2022). Evaluation of the TruSight Oncology 500 Assay for routine clinical trials of tumor mutational burden and clinical utility for predicting response to pembrolizumab. Journal of Molecular Diagnostics: JMD, twenty four(6), 600–608. https://doi.org/10.1016/j.jmoldx.2022.01.008
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